hdf5 url does not seems to work

[picca]

Hello, I try to open this file, like this

fabio_viewer hdf5:///nfs/ruche-diffabs/diffabs-soleil/com-diffabs/2016/Run4/2016-09-01/IHR_30.nxs?scan_30/scan_data/data_02

fabio do not detect this as a known uri.

but

If I use

fabio_viewer /nfs/ruche-diffabs/diffabs-soleil/com-diffabs/2016/Run4/2016-09-01/IHR_30.nxs::scan_30/scan_data/data_02

it works.

So my question is whcih version is the right one ?

[vallsv]

AFAIK we do not support URI

Is the one with hdf5:FILENAME?PATH normalized somewhere?

[picca]

here the link from fabio

http://sources.debian.net/src/python-fabio/0.4.0%2Bdfsg-2/fabio/openimage.py/#L172

but it seems to me that this is not implemented.

[vallsv]

We decide to support :: from this URI format https://github.com/blaze/odo/blob/master/docs/source/uri.rst, but it does not allow to create slicing.

I think the one from the documentation was only informative and not implemented.

[vallsv]

If some kind or generic URI exists it can be very useful.

[vallsv]

In [26]: fabio.open("hdf5:///workspace/valls/silx.git/alltypes_GmKvnA.h5::/")
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-26-2e123c93db8d> in <module>()
----> 1 fabio.open("hdf5:///workspace/valls/silx.git/alltypes_GmKvnA.h5::/")

/home/valls/.local/lib/python2.7/site-packages/fabio/openimage.pyc in openimage(filename, frame)
    134     else:
    135         logger.debug("Attempting to open %s" % (filename))
--> 136         obj = _openimage(filename)
    137         logger.debug("Attempting to read frame %s from %s with reader %s" % (frame, filename, obj.classname))
    138         obj = obj.read(obj.filename, frame)

/home/valls/.local/lib/python2.7/site-packages/fabio/openimage.pyc in _openimage(filename)
    212 
    213     if url.scheme in ["nxs", "hdf5"] and filetype == "hdf5":
--> 214         obj.set_url(url)
    215     obj.filename = filename
    216     # skip the read for read header

AttributeError: 'Hdf5Image' object has no attribute 'set_url'

It looks to be unimplemented.

[picca]

I am wondering if the guyes from taurus did not already implemented something like this ?

[vallsv]

My bad, that's a mixed syntax...

[picca]

what about this http://h5serv.readthedocs.io/en/latest/index.html

[vallsv]

I don't think it provides any URL format with a slicing.

[picca]

I just contacted carlos pascal from taurus in order to have its opinion. they have a scheme for their data sources. And I think that it could nice to share the same between silx/fabio/pyFAI and taurus. To avoid two different syntax

[picca]

Here an example of url with a slice whci his in fact select :)

https://data.hdfgroup.org:7258/datasets/4af8bc72-3e8a-11e6-a48f-0242ac110003/value?host=tall.data.hdfgroup.org&select=[0:4,0:4]

[picca]

Here the h5file-scheme whcih was discussed with armando a time ago :)

https://github.com/taurus-org/h5file-scheme

[vallsv]

BTW, i don't think it is a very good idea to use fabio to open a HDF5 file. It can be useful first, but i am afraid it will create an useless overhead on top of h5py.